Using eDNA to understand predator-prey interactions influenced by invasive species.

Invasive predatory species may alter population dynamic processes of their prey and impact biological communities and ecosystem processes. Revealing biotic interactions, however, including the relationship between predator and prey, is a difficult task, in particular for species that are hard to monitor. Here, we present a case study that documents the utility of environmental DNA analysis (eDNA) to assess predator-prey interactions between two invasive fishes (Lepomis gibbosus, Pseudorasbora parva) and two potential amphibian prey species, (Triturus cristatus, Pelobates fuscus). We used species-specific TaqMan assays for quantitative assessment of eDNA concentrations from water samples collected from 89 sites across 31 ponds during three consecutive months from a local amphibian hotspot in Germany. We found a negative relationship between eDNA concentrations of the predators (fishes) and prey (amphibians) using Monte-Carlo tests. Our study highlights the potential of eDNA application to reveal predator-prey interactions and confirms the hypothesis that the observed local declines of amphibian species may be at least partly caused by recently introduced invasive fishes. Our findings have important consequences for local conservation management and highlight the usefulness of eDNA approaches to assess ecological interactions and guide targeted conservation action.

Could climate change benefit invasive snakes? Modelling the potential distribution of the California Kingsnake in the Canary Islands.

The interaction between climate change and biological invasions is a global conservation challenge with major consequences for invasive species management. However, our understanding of this interaction has substantial knowledge gaps; this is particularly relevant for invasive snakes on islands because they can be a serious threat to island ecosystems. Here we evaluated the potential influence of climate change on the distribution of invasive snakes on islands, using the invasion of the California kingsnake (Lampropeltis californiae) in Gran Canaria. We analysed the potential distribution of L. californiae under current and future climatic conditions in the Canary Islands, with the underlying hypothesis that the archipelago might be suitable for the species under these climate scenarios. Our results indicate that the Canary Islands are currently highly suitable for the invasive snake, with increased suitability under the climate change scenarios tested here. This study supports the idea that invasive reptiles represent a substantial threat to near-tropical regions, and builds on previous studies suggesting that the menace of invasive reptiles may persist or even be exacerbated by climate change. We suggest future research should continue to fill the knowledge gap regarding invasive reptiles, in particular snakes, to clarify their potential future impacts on global biodiversity.

Identifying early modern human ecological niche expansions and associated cultural dynamics in the South African Middle Stone Age.

The archaeological record shows that typically human cultural traits emerged at different times, in different parts of the world, and among different hominin taxa. This pattern suggests that their emergence is the outcome of complex and nonlinear evolutionary trajectories, influenced by environmental, demographic, and social factors, that need to be understood and traced at regional scales. The application of predictive algorithms using archaeological and paleoenvironmental data allows one to estimate the ecological niches occupied by past human populations and identify niche changes through time, thus providing the possibility of investigating relationships between cultural innovations and possible niche shifts. By using such methods to examine two key southern Africa archaeological cultures, the Still Bay [76-71 thousand years before present (ka)] and the Howiesons Poort (HP; 66-59 ka), we identify a niche shift characterized by a significant expansion in the breadth of the HP ecological niche. This expansion is coincident with aridification occurring across Marine Isotope Stage 4 (ca. 72-60 ka) and especially pronounced at 60 ka. We argue that this niche shift was made possible by the development of a flexible technological system, reliant on composite tools and cultural transmission strategies based more on "product copying" rather than "process copying." These results counter the one niche/one human taxon equation. They indicate that what makes our cultures, and probably the cultures of other members of our lineage, unique is their flexibility and ability to produce innovations that allow a population to shift its ecological niche.

RWTY (R We There Yet): An R Package for Examining Convergence of Bayesian Phylogenetic Analyses.

Bayesian inference using Markov chain Monte Carlo (MCMC) has become one of the primary methods used to infer phylogenies from sequence data. Assessing convergence is a crucial component of these analyses, as it establishes the reliability of the posterior distribution estimates of the tree topology and model parameters sampled from the MCMC. Numerous tests and visualizations have been developed for this purpose, but many of the most popular methods are implemented in ways that make them inconvenient to use for large data sets. RWTY is an R package that implements established and new methods for diagnosing phylogenetic MCMC convergence in a single convenient interface.

Eyes Wide Shut: the impact of dim-light vision on neural investment in marine teleosts.

Understanding how organismal design evolves in response to environmental challenges is a central goal of evolutionary biology. In particular, assessing the extent to which environmental requirements drive general design features among distantly related groups is a major research question. The visual system is a critical sensory apparatus that evolves in response to changing light regimes. In vertebrates, the optic tectum is the primary visual processing centre of the brain and yet it is unclear how or whether this structure evolves while lineages adapt to changes in photic environment. On one hand, dim-light adaptation is associated with larger eyes and enhanced light-gathering power that could require larger information processing capacity. On the other hand, dim-light vision may evolve to maximize light sensitivity at the cost of acuity and colour sensitivity, which could require less processing power. Here, we use X-ray microtomography and phylogenetic comparative methods to examine the relationships between diel activity pattern, optic morphology, trophic guild and investment in the optic tectum across the largest radiation of vertebrates-teleost fishes. We find that despite driving the evolution of larger eyes, enhancement of the capacity for dim-light vision generally is accompanied by a decrease in investment in the optic tectum. These findings underscore the importance of considering diel activity patterns in comparative studies and demonstrate how vision plays a role in brain evolution, illuminating common design principles of the vertebrate visual system.

Whole Exon Deletion in the GFAP Gene Is a Novel Molecular Mechanism Causing Alexander Disease.

Alexander disease (AD) is a leukodystrophy caused by heterozygous mutations in the gene encoding the glial fibrillary acidic protein (GFAP). Currently, de novo heterozygous missense mutations in the GFAP gene are identified in over 95% of patients with AD. However, patients with biopsy-proven AD have been reported in whom no GFAP mutation has been identified. We report identical twin boys presenting in infancy with seizures and developmental delay in whom MR appearances were suggestive of AD with the exception of an unusual, bilateral, arc of calcification at the frontal white-gray junction. Initial mutation screening of the GFAP gene did not identify a mutation. Whole exome sequencing in both brothers revealed a de novo heterozygous in-frame deletion of the whole of exon 5 of the GFAP gene. Mutations in the GFAP gene are thought to result in a toxic effect of mutant GFAP disrupting the formation of the normal intermediate filament network and resulting in Rosenthal fiber formation, which has hitherto not been linked to exonic scale copy number variants in GFAP. Further studies on mutation negative AD patients are warranted to determine whether a similar mechanism underlies their disease.

Longevity Is Linked to Mitochondrial Mutation Rates in Rockfish: A Test Using Poisson Regression.

The mitochondrial theory of ageing proposes that the cumulative effect of biochemical damage in mitochondria causes mitochondrial mutations and plays a key role in ageing. Numerous studies have applied comparative approaches to test one of the predictions of the theory: That the rate of mitochondrial mutations is negatively correlated with longevity. Comparative studies face three challenges in detecting correlates of mutation rate: Covariation of mutation rates between species due to ancestry, covariation between life-history traits, and difficulty obtaining accurate estimates of mutation rate. We address these challenges using a novel Poisson regression method to examine the link between mutation rate and lifespan in rockfish (Sebastes). This method has better performance than traditional sister-species comparisons when sister species are too recently diverged to give reliable estimates of mutation rate. Rockfish are an ideal model system: They have long life spans with indeterminate growth and little evidence of senescence, which minimizes the confounding tradeoffs between lifespan and fecundity. We show that lifespan in rockfish is negatively correlated to rate of mitochondrial mutation, but not the rate of nuclear mutation. The life history of rockfish allows us to conclude that this relationship is unlikely to be driven by the tradeoffs between longevity and fecundity, or by the frequency of DNA replications in the germline. Instead, the relationship is compatible with the hypothesis that mutation rates are reduced by selection in long-lived taxa to reduce the chance of mitochondrial damage over its lifespan, consistent with the mitochondrial theory of ageing.

Projecting future expansion of invasive species: comparing and improving methodologies for species distribution modeling.

Modeling the distributions of species, especially of invasive species in non-native ranges, involves multiple challenges. Here, we developed some novel approaches to species distribution modeling aimed at reducing the influences of such challenges and improving the realism of projections. We estimated species-environment relationships for Parthenium hysterophorus L. (Asteraceae) with four modeling methods run with multiple scenarios of (i) sources of occurrences and geographically isolated background ranges for absences, (ii) approaches to drawing background (absence) points, and (iii) alternate sets of predictor variables. We further tested various quantitative metrics of model evaluation against biological insight. Model projections were very sensitive to the choice of training dataset. Model accuracy was much improved using a global dataset for model training, rather than restricting data input to the species' native range. AUC score was a poor metric for model evaluation and, if used alone, was not a useful criterion for assessing model performance. Projections away from the sampled space (i.e., into areas of potential future invasion) were very different depending on the modeling methods used, raising questions about the reliability of ensemble projections. Generalized linear models gave very unrealistic projections far away from the training region. Models that efficiently fit the dominant pattern, but exclude highly local patterns in the dataset and capture interactions as they appear in data (e.g., boosted regression trees), improved generalization of the models. Biological knowledge of the species and its distribution was important in refining choices about the best set of projections. A post hoc test conducted on a new Parthenium dataset from Nepal validated excellent predictive performance of our 'best' model. We showed that vast stretches of currently uninvaded geographic areas on multiple continents harbor highly suitable habitats for parthenium. However, discrepancies between model predictions and parthenium invasion in Australia indicate successful management for this globally significant weed.

Intracranial calcification in childhood: a review of aetiologies and recognizable phenotypes.

Intracranial calcification (ICC) is a common finding on neuroimaging in paediatric neurology practice. In approximately half of all cases the calcification occurs in damaged, neoplastic, or malformed brain. For the large number of other disorders in which ICC occurs, no common pathogenetic mechanism can be suggested. Congenital infection, particularly with cytomegalovirus, accounts for a significant proportion of all cases. However, some genetic diseases, in particular Aicardi-Goutières syndrome, Band-like calcification, and RNASET2-related disease, may mimic congenital infection; therefore, a full consideration of the radiological and clinical features is necessary before concluding that congenital infection is the cause. In some disorders calcification is a universal finding, in others it is a frequent occurrence, and in some it is only an occasional finding. Characteristic patterns of calcification are seen in a number of conditions, and a systematic approach to the identification and description of radiological findings, taken together in the context of the clinical scenario, allows a diagnosis to be made in many cases. Nonetheless, there remain a number of presumed genetic disorders associated with ICC for which the underlying molecular cause has not yet been identified.

Evolution of cold-tolerant fungal symbionts permits winter fungiculture by leafcutter ants at the northern frontier of a tropical ant-fungus symbiosis.

The obligate mutualism between leafcutter ants and their Attamyces fungi originated 8 to 12 million years ago in the tropics, but extends today also into temperate regions in South and North America. The northernmost leafcutter ant Atta texana sustains fungiculture during winter temperatures that would harm the cold-sensitive Attamyces cultivars of tropical leafcutter ants. Cold-tolerance of Attamyces cultivars increases with winter harshness along a south-to-north temperature gradient across the range of A. texana, indicating selection for cold-tolerant Attamyces variants along the temperature cline. Ecological niche modeling corroborates winter temperature as a key range-limiting factor impeding northward expansion of A. texana. The northernmost A. texana populations are able to sustain fungiculture throughout winter because of their cold-adapted fungi and because of seasonal, vertical garden relocation (maintaining gardens deep in the ground in winter to protect them from extreme cold, then moving gardens to warmer, shallow depths in spring). Although the origin of leafcutter fungiculture was an evolutionary breakthrough that revolutionized the food niche of tropical fungus-growing ants, the original adaptations of this host-microbe symbiosis to tropical temperatures and the dependence on cold-sensitive fungal symbionts eventually constrained expansion into temperate habitats. Evolution of cold-tolerant fungi within the symbiosis relaxed constraints on winter fungiculture at the northern frontier of the leafcutter ant distribution, thereby expanding the ecological niche of an obligate host-microbe symbiosis.

Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei: Beryciformes: Holocentridae): reconciling more than 100 years of taxonomic confusion.

Squirrelfishes and soldierfishes (Holocentridae) are among the most conspicuous species in the nocturnal reef fish community. However, there is no clear consensus regarding their evolutionary relationships, which is reflected in a complicated taxonomic history. We collected DNA sequence data from multiple single copy nuclear genes and one mitochondrial gene sampled from over fifty percent of the recognized holocentrid species and infer the first species-level phylogeny of the Holocentridae. Our results strongly support the monophyly of the clades Myripristinae (soldierfishes) and Holocentrinae (squirrelfishes). The molecular phylogenies differ with regard to previous hypotheses of relationships within the Myriprisitinae, resolving a clade of cryptic reef associated and deep water non-reef dwelling lineages (Corniger+Plectrypops+Ostichthys) that is the sister lineage to a monophyletic Myripristis. Within Holocentrinae, Neoniphon and Sargocentron are strongly supported as paraphyletic, while Holocentrus is nested within Sargocentron. Using Bayesian ancestral state reconstruction methods, we demonstrate the taxonomically diagnostic characters for Neoniphon and Sargocentron likely represent character states with a complex evolutionary history that is not reflective of shared common ancestry. We propose a new classification for Holocentrinae, recognizing four lineages that are treated as genera: Sargocentron Fowler, 1904, Holocentrus Scopoli, 1777, Flameo Jordan and Evermann, 1898, and Neoniphon Castelnau, 1875.

Ecological niche modeling in Maxent: the importance of model complexity and the performance of model selection criteria.

Maxent, one of the most commonly used methods for inferring species distributions and environmental tolerances from occurrence data, allows users to fit models of arbitrary complexity. Model complexity is typically constrained via a process known as L1 regularization, but at present little guidance is available for setting the appropriate level of regularization, and the effects of inappropriately complex or simple models are largely unknown. In this study, we demonstrate the use of information criterion approaches to setting regularization in Maxent, and we compare models selected using information criteria to models selected using other criteria that are common in the literature. We evaluate model performance using occurrence data generated from a known "true" initial Maxent model, using several different metrics for model quality and transferability. We demonstrate that models that are inappropriately complex or inappropriately simple show reduced ability to infer habitat quality, reduced ability to infer the relative importance of variables in constraining species' distributions, and reduced transferability to other time periods. We also demonstrate that information criteria may offer significant advantages over the methods commonly used in the literature.

Climate change may induce connectivity loss and mountaintop extinction in Central American forests.

The tropical forests of Central America serve a pivotal role as biodiversity hotspots and provide ecosystem services securing human livelihood. However, climate change is expected to affect the species composition of forest ecosystems, lead to forest type transitions and trigger irrecoverable losses of habitat and biodiversity. Here, we investigate potential impacts of climate change on the environmental suitability of main plant functional types (PFTs) across Central America. Using a large database of occurrence records and physiological data, we classify tree species into trait-based groups and project their suitability under three representative concentration pathways (RCPs 2.6, 4.5 and 8.5) with an ensemble of state-of-the-art correlative modelling methods. Our results forecast transitions from wet towards generalist or dry forest PFTs for large parts of the study region. Moreover, suitable area for wet-adapted PFTs is projected to latitudinally diverge and lose connectivity, while expected upslope shifts of montane species point to high risks of mountaintop extinction. These findings underline the urgent need to safeguard the connectivity of habitats through biological corridors and extend protected areas in the identified transition hotspots.

The squirrel is in the detail: Anatomy and morphometry of the tail in Sciuromorpha (Rodentia, Mammalia).

In mammals, the caudal vertebrae are certainly among the least studied elements of their skeleton. However, the tail plays an important role in locomotion (e.g., balance, prehensility) and behavior (e.g., signaling). Previous studies largely focused on prehensile tails in Primates and Carnivora, in which certain osteological features were selected and used to define tail regions (proximal, transitional, distal). Interestingly, the distribution pattern of these anatomical characters and the relative proportions of the tail regions were similar in both orders. In order to test if such tail regionalization can be applied to Rodentia, we investigated the caudal vertebrae of 20 Sciuridae and six Gliridae species. Furthermore, we examined relationships between tail anatomy/morphometry and locomotion. The position of selected characters along the tail was recorded and their distribution was compared statistically using Spearman rank correlation. Vertebral body length (VBL) was measured to calculate the proportions of each tail region and to perform procrustes analysis on the shape of relative vertebral body length (rVBL) progressions. Our results show that tail regionalization, as defined for Primates and Carnivora, can be applied to almost all investigated squirrels, regardless of their locomotor category. Moreover, major locomotor categories can be distinguished by rVBL progression and tail region proportions. In particular, the small flying squirrels Glaucomys volans and Hylopetes sagitta show an extremely short transitional region. Likewise, several semifossorial taxa can be distinguished by their short distal region. Moreover, among flying squirrels, Petaurista petaurista shows differences with the small flying squirrels, mirroring previous observations on locomotory adaptations based on their inner ear morphometry. Our results show furthermore that the tail region proportions of P. petaurista, phylogenetically more basal than the small flying squirrels, are similar to those of bauplan-conservative arboreal squirrels.

Reevaluating claims of ecological speciation in Halichoeres bivittatus.

Allopatry has traditionally been viewed as the primary driver of speciation in marine taxa, but the geography of the marine environment and the larval dispersal capabilities of many marine organisms render this view somewhat questionable. In marine fishes, one of the earliest and most highly cited empirical examples of ecological speciation with gene flow is the slippery dick wrasse, Halichoeres bivittatus. Evidence for this cryptic or incipient speciation event was primarily in the form of a deep divergence in a single mitochondrial locus between the northern and southern Gulf of Mexico, combined with a finding that these two haplotypes were associated with different habitat types ("tropical" vs. "subtropical") in the Florida Keys and Bermuda, where they overlap. Here, we examine habitat assortment in the Florida Keys using a broader sampling of populations and habitat types than were available for the original study. We find no evidence to support the claim that haplotype frequencies differ between habitat types, and little evidence to support any differences between populations in the Keys. These results undermine claims of ecological speciation with gene flow in Halichoeres bivittatus. Future claims of this type should be supported by multiple lines of evidence that illuminate potential mechanisms and allow researchers to rule out alternative explanations for spatial patterns of genetic differences.

Comparing the dietary niche overlap and ecomorphological differences between invasive Hemidactylus mabouia geckos and a native gecko competitor.

Hemidactylus mabouia is one of the most successful, widespread invasive reptile species and has become ubiquitous across tropical urban settings in the Western Hemisphere. Its ability to thrive in close proximity to humans has been linked to the rapid disappearance of native geckos. However, aspects of Hemidactylus mabouia natural history and ecomorphology, often assumed to be linked with this effect on native populations, remain understudied or untested. Here, we combine data from ∂15N and ∂13C stable isotopes, stomach contents, and morphometric analyses of traits associated with feeding and locomotion to test alternate hypotheses of displacement between H. mabouia and a native gecko, Phyllodactylus martini, on the island of Curaçao. We demonstrate substantial overlap of invertebrate prey resources between the species, with H. mabouia stomachs containing larger arthropod prey as well as vertebrate prey. We additionally show that H. mabouia possesses several morphological advantages, including larger sizes in feeding-associated traits and limb proportions that could offer a propulsive locomotor advantage on vertical surfaces. Together, these findings provide the first support for the hypotheses that invasive H. mabouia and native P. martini overlap in prey resources and that H. mabouia possess ecomorphological advantages over P. martini. This work provides critical context for follow-up studies of H. mabouia and P. martini natural history and direct behavioral experiments that may ultimately illuminate the mechanisms underlying displacement on this island and act as a potential model for other systems with Hemidactylus mabouia invasions.

Homoplasy and clade support.

Distinguishing phylogenetic signal from homoplasy (shared similarities among taxa that do not arise by common ancestry) is an implicit goal of any phylogenetic study. Large amounts of homoplasy can interfere with accurate tree inference, and it is expected that common measures of clade support, including bootstrap proportions and Bayesian posterior probabilities, should also be impacted to some degree by homoplasy. Through data simulation and analysis of 38 empirical data sets, we show that high amounts of homoplasy will affect all measures of clade support in a manner that is dependent on clade size. More specifically, the smallest taxon bipartitions in an unrooted tree topology will receive higher support relative to clades of intermediate sizes, even when all clades are supported by the same amount of data. We determine that the ultimate causes of this effect are the inclusion of random trees (due to homoplasy) during bootstrap resampling and Markov chain Monte Carlo (MCMC) topology searching and the higher relative proportion of small taxon bipartitions (i.e., 2 or 3 taxa) to larger sized bipartitions. However, the use of explicit model-based methods, especially Bayesian MCMC methods, effectively overcomes this clade size effect even when very small amounts of phylogenetic signal are present. We develop a post hoc statistic, the clade disparity index (CDI), to measure both the relative magnitude of the clade size effect and its statistical significance. In analyses of both simulated and empirical data, CDI values indicate that Bayesian MCMC analyses are substantially more likely to estimate clade support values that are uncorrelated with clade size than are maximum parsimony and maximum likelihood bootstrap analyses and thus less affected by homoplasy. These results may be especially relevant to "deep" phylogenetic problems, such as reconstructing the tree of life, as they represent the largest possible extremes of time and evolutionary rates, 2 factors that cause homoplasy.

AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics.

UNLABELLED: A key element to a successful Markov chain Monte Carlo (MCMC) inference is the programming and run performance of the Markov chain. However, the explicit use of quality assessments of the MCMC simulations-convergence diagnostics-in phylogenetics is still uncommon. Here, we present a simple tool that uses the output from MCMC simulations and visualizes a number of properties of primary interest in a Bayesian phylogenetic analysis, such as convergence rates of posterior split probabilities and branch lengths. Graphical exploration of the output from phylogenetic MCMC simulations gives intuitive and often crucial information on the success and reliability of the analysis. The tool presented here complements convergence diagnostics already available in other software packages primarily designed for other applications of MCMC. Importantly, the common practice of using trace-plots of a single parameter or summary statistic, such as the likelihood score of sampled trees, can be misleading for assessing the success of a phylogenetic MCMC simulation. AVAILABILITY: The program is available as source under the GNU General Public License and as a web application at http://ceb.scs.fsu.edu/awty.

Latitudinal and bathymetrical species richness patterns in the NW Pacific and adjacent Arctic Ocean.

Global scale analyses have recently revealed that the latitudinal gradient in marine species richness is bimodal, peaking at low-mid latitudes but with a dip at the equator; and that marine species richness decreases with depth in many taxa. However, these overall and independently studied patterns may conceal regional differences that help support or qualify the causes in these gradients. Here, we analysed both latitudinal and depth gradients of species richness in the NW Pacific and its adjacent Arctic Ocean. We analysed 324,916 distribution records of 17,414 species from 0 to 10,900 m depth, latitude 0 to 90°N, and longitude 100 to 180°N. Species richness per c. 50 000 km2 hexagonal cells was calculated as alpha (local average), gamma (regional total) and ES50 (estimated species for 50 records) per latitudinal band and depth interval. We found that average ES50 and gamma species richness decreased per 5° latitudinal bands and 100 m depth intervals. However, average ES50 per hexagon showed that the highest species richness peaked around depth 2,000 m where the highest total number of species recorded. Most (83%) species occurred in shallow depths (0 to 500 m). The area around Bohol Island in the Philippines had the highest alpha species richness (more than 8,000 species per 50,000 km2). Both alpha and gamma diversity trends increased from the equator to latitude 10°N, then further decreased, but reached another peak at higher latitudes. The latitudes 60-70°N had the lowest gamma and alpha diversity where there is almost no ocean in our study area. Model selection on Generalized Additive Models (GAMs) showed that the combined effects of all environmental predictors produced the best model driving species richness in both shallow and deep sea. The results thus support recent hypotheses that biodiversity, while highest in the tropics and coastal depths, is decreasing at the equator and decreases with depth below ~2000 m. While we do find the declines of species richness with latitude and depth that reflect temperature gradients, local scale richness proved poorly correlated with many environmental variables. This demonstrates that while regional scale patterns in species richness may be related to temperature, that local scale richness depends on a greater variety of variables.

Niche Estimation Above and Below the Species Level.

Ecological niches reflect not only adaptation to local circumstances but also the tendency of related lineages to share environmental tolerances. As a result, information on phylogenetic relationships has underappreciated potential to inform ecological niche modeling. Here we review three strategies for incorporating evolutionary information into niche models: splitting lineages into subunits, lumping across lineages, and partial pooling of lineages into a common statistical framework that implicitly or explicitly accounts for evolutionary relationships. We challenge the default practice of modeling at the species level, which ignores the process of niche evolution and erroneously assumes that the species is always the appropriate level for niche estimation. Progress in the field requires reexamination of how we assess models of niches versus models of distributions.